Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015425.1 Corchorus olitorius cultivar O-4 contig15458, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 59216
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4319 original size:2 final size:2
Alignment explanation
Indices: 4314--4338 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4304 TTTTTTTGGT
4314 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
4339 TCAGGTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:18610 original size:2 final size:2
Alignment explanation
Indices: 18603--18629 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18593 CTGACCTAGC
18603 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
18630 GCTTAGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32390 original size:2 final size:2
Alignment explanation
Indices: 32383--32408 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32373 GCAATAATGC
32383 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
32409 CTAATCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36027 original size:10 final size:10
Alignment explanation
Indices: 36012--36036 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
36002 TCACCCCCTC
36012 AAAAAAAAGA
1 AAAAAAAAGA
36022 AAAAAAAAGA
1 AAAAAAAAGA
36032 AAAAA
1 AAAAA
36037 GAAAAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:42160 original size:57 final size:57
Alignment explanation
Indices: 42072--42180 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
42062 TTCTGCATGG
* * **
42072 TTTGGCAACTGCAGAGGGCGAAAAAGCACAGACATCACATGCTGTTGCTCAGTATGA
1 TTTGGCAACTGCAGAGGACGAAAAAGCACAGACATCAAATGCCATTGCTCAGTATGA
* *
42129 TTTGGCAACTTCAGAGGACGAGAATA-CACAGACATCAAATGCCATTGCTCAG
1 TTTGGCAACTGCAGAGGACGA-AAAAGCACAGACATCAAATGCCATTGCTCAG
42181 CATGGCTTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 42 0.93
58 3 0.07
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (57 bp):
TTTGGCAACTGCAGAGGACGAAAAAGCACAGACATCAAATGCCATTGCTCAGTATGA
Found at i:46293 original size:51 final size:51
Alignment explanation
Indices: 46233--46334 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
46223 TATCATAAGA
46233 TAATTTGTTAAAGATGTTTCAAAGGCAGGAATAGTTTGGTTTTGAGTTTTG
1 TAATTTGTTAAAGATGTTTCAAAGGCAGGAATAGTTTGGTTTTGAGTTTTG
46284 TAATTTGTTAAAGATGTTTCAAAGGCAGGAATAGTTTGGTTTTGAGTTTTG
1 TAATTTGTTAAAGATGTTTCAAAGGCAGGAATAGTTTGGTTTTGAGTTTTG
46335 ATGAAATGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.04, G:0.25, T:0.43
Consensus pattern (51 bp):
TAATTTGTTAAAGATGTTTCAAAGGCAGGAATAGTTTGGTTTTGAGTTTTG
Found at i:54384 original size:9 final size:9
Alignment explanation
Indices: 54362--54405 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
54352 TGAAGGTTTA
*
54362 TTTTTGTTTT
1 TTTTT-TTTG
54372 TTTTTTTTG
1 TTTTTTTTG
54381 -TTTTTTTG
1 TTTTTTTTG
*
54389 TTATTTTTG
1 TTTTTTTTG
54398 TTTTTTTT
1 TTTTTTTT
54406 TTTACCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
8 8 0.27
9 17 0.57
10 5 0.17
ACGTcount: A:0.02, C:0.00, G:0.09, T:0.89
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:54416 original size:30 final size:30
Alignment explanation
Indices: 54359--54416 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
54349 TGATGAAGGT
***
54359 TTATTTTTGTTTTTTTTTTTTGTTTTTTTG
1 TTATTTTTGTTTTTTTTTTTACCTTTTTTG
54389 TTATTTTTGTTTTTTTTTTTACCTTTTT
1 TTATTTTTGTTTTTTTTTTTACCTTTTT
54417 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.05, C:0.03, G:0.07, T:0.84
Consensus pattern (30 bp):
TTATTTTTGTTTTTTTTTTTACCTTTTTTG
Found at i:55966 original size:14 final size:14
Alignment explanation
Indices: 55947--55975 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
55937 ATACTCAATC
55947 TATTGTAATTATTA
1 TATTGTAATTATTA
55961 TATTGTAATTATTA
1 TATTGTAATTATTA
55975 T
1 T
55976 GAGTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TATTGTAATTATTA
Found at i:56631 original size:335 final size:333
Alignment explanation
Indices: 55985--58974 Score: 4486
Period size: 332 Copynumber: 9.0 Consensus size: 333
55975 TGAGTATATA
* *
55985 TTAATTAGAAATTAATTCGGAAAAAATTAGGAAAAACGATAATTGAAGTGTCTAAAGCCCTTCAA
1 TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAA
* * *
56050 TCTTTTTGGACTTGAATTATATATTTTATATGAATGTTGTGGCCAAAAATTGAGGACAAATTTTT
66 TCTTTTTGGACTTGAATTATATATTTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTTTT
* *
56115 CAGGACAGTTTTTGCAAAATTTTGTTCGAAATTGTGTACTAACCATCACAGTTTTTGGCTAAAAA
131 CGGGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAA
*
56180 CGCGTTCCTGGGCACCGGCACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAA
196 CGCGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAA
56245 ATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTAT
261 ATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTAT
56310 AATTCGAT
326 AATTCGAT
56318 TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAAAACGATAATTGAAGCGTCTAAAGCCCTTC
1 TTAATTAGAAATTAATTCGGGAAAAATTAGG--AAAAACGATAATTGAAGCGTCTAAAGCCCTTC
* * *
56383 AATCTTTTTGGACTTGAGTTATATATTTTTTATGAATGTTCTGGCCTAAAATTGAGGAAAAATTA
64 AATCTTTTTGGACTTGAATTATATATTTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTT
* * *
56448 TTCGGGACAGTTTTTGCAAAATTTTGCTCGAAATCGTGTACTTACTATCACAGTTTTTGGCTAAA
129 TTCGGGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAA
* *
56513 AACGCGTTCCTGGGCACCAACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCGTTAAAATATGT
194 AACGCGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGT
* * *
56578 AAATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAAGGTTTTACGACCATCTGAATT
259 AAATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATT
56643 ATAATTCGAT
324 ATAATTCGAT
* *** * * *
56653 TTAATTAAAAATTAATT-TATAAAAA-TAGAAAAAACGAT-ATTAGAA--TTCTGAAAAGCCATT
1 TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATT-GAAGCGTCT--AAAGCCCTT
* * * ** * * *
56713 -AAGT-TTTATT-GCCGTTGAGTTATATATTTTTTATGAGTACTGTGGCTAAAAATTAAGGAAAA
63 CAA-TCTTT-TTGGAC-TTGAATTATATATTTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAA
* ** * *
56775 ATTTTTTGAAACAGTTTTTGCAAAATTTTG-ACCAAATCGTGTACTAACCATCACAGTTTTTGGC
125 ATTTTTCGGGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTACTAACCATCACAGTTTTTGGC
* * * * ** * * ** *
56839 TAAAAAGGTGCTCCTGGGGC-CCGGCACAGTTTTGCATGATTTTTGG-GGCCAGTGTCAC-TGAA
190 TAAAAACGCGTTCCT-GGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTC-CTTAAA
* * * * * * * * ** ** *
56901 ATATCTACATTCATCTAACTAATTCTTAGCCACATTGGATTTATGGTTTTGTTTTTACGAGCATC
253 ATATGTAAATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGGCTTTACGACCATC
* **
56966 TGAATCATGTTTCGAT
318 TGAATTATAATTCGAT
* *
56982 TTAATTAGAAATTAATTCGGAAAAAATTAGGAAAAACAATAATTGAAGCGTCTAAAGCCCTTCAA
1 TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAA
*
57047 TCTTTTTGGACTTGAATTAAATA-TTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTTTT
66 TCTTTTTGGACTTGAATTATATATTTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTTTT
* * **
57111 CGAGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTACTTTACCATCTTAG-TTTTGGCTAAAA
131 CGGGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTAC-TAACCATCACAGTTTTTGGCTAAAA
*
57175 ACGTGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTA
195 ACGCGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTA
57240 AATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTA
260 AATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTA
57305 TAATTCGAT
325 TAATTCGAT
57314 TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAA
1 TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAA
* *
57379 TCTTTTTGAACTTGAATTATATATTTTTTTATGAATGTTCTGGCCAAAAACTGAGGAAAAATTTT
66 TCTTTTTGGACTTGAATTATATA-TTTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTTT
* **
57444 TCGAGACAGTTTTTGCAAAATTTTGTTCGAAATCGTG---T---CATCACAGTTTTTATCTAAAA
130 TCGGGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAA
*
57503 ACGCGTTCCTGGACACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCC-TAAAATATGTA
195 ACGCGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTA
* * *
57567 AATTCATCTAACCAAATCTCAGCCACAATGGATTTATAGATAAGGCTTTACGATCATCTGAATTA
260 AATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTA
57632 TAATTCGAT
325 TAATTCGAT
* *
57641 TTAATGAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCATCAA
1 TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAA
* * *
57706 TCTTTTTGGACTTGAATTATATAATTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTT
66 TCTTTTTGGACTTGAATTATATATTTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTTTT
*
57771 CGGGACAGTTTTTGCAAAA---T-TT-G-----GT-T-CGAA-CATCACAG-TTTTGGCTAAAAA
131 CGGGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAA
57822 CGCGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAA
196 CGCGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAA
* * *
57887 ATTCATCTGACCAAATCTTAGCCACAATGGATTTATGGATAAGTCTTTACGGCCATCTGAATTAT
261 ATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTAT
57952 AATTCGAT
326 AATTCGAT
* * *
57960 TTAATCAGAAATTAATTCTGGAAAAATTAGGAAAAACGATAATTGAAGCGTCAAAAGCCCTTCAA
1 TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAA
* * * * *
58025 TCTTATTGGACTTGAATTATATAATTTTTATGAGTGTTGTGGCCAAAAATTGAGTAAAAATTTTT
66 TCTTTTTGGACTTGAATTATATATTTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTTTT
* * * *
58090 CGGGAGAGTTTTTTCAAAATTTTGTTCGAAATCGTATACTTACCATCACAACAGTTTTTGGCTAA
131 CGGGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTACTAACCAT--C-ACAGTTTTTGGCTAA
*
58155 AAACGCGTTCCTGGGCACCGACACAGTTTTGGATGATTTTTGGCAGCAAGACTCCTTAAAATATG
193 AAACGCGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATG
* *
58220 TAAATTAATCTGACCAAATCTCAGCCACAATGGATTTAAGGATAAGGCTTTACGACCATCTGAAT
258 TAAATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAAT
58285 TATAATTCGAT
323 TATAATTCGAT
* * *
58296 TTAATCAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCAAAAGCCCATCAA
1 TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAA
* *
58361 TCGTTTTGGACTTGAATTATAAATTTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTTTT
66 TCTTTTTGGACTTGAATTATATATTTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTTTT
*
58426 CGGGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAA
131 CGGGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAA
58491 CGCGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAA
196 CGCGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAA
*
58556 ATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGTCTTTACGACCATCTGAATTAT
261 ATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTAT
58621 AATTCGAT
326 AATTCGAT
58629 TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAA
1 TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAA
58694 TCTTTTTGGACTTGAATTATATA-TTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTTTT
66 TCTTTTTGGACTTGAATTATATATTTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTTTT
* *
58758 CGGGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTACTAACTATCACAGTTTTTTGCTAAAAA
131 CGGGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAA
*
58823 CGCGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGCCTCCTTAAAATATGTAA
196 CGCGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAA
* * * * *
58888 ATTAATCTAACCAAATCTCAGCCACAATGGATTTATGGGTAAGGCTTTACGACCATATGAATTTT
261 ATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTAT
*
58953 ATTTCGAT
326 AATTCGAT
58961 TTAATTAGAAATTA
1 TTAATTAGAAATTA
58975 GGGTTTTGTT
Statistics
Matches: 2409, Mismatches: 200, Indels: 97
0.89 0.07 0.04
Matches are distributed among these distances:
316 2 0.00
318 62 0.03
319 228 0.09
321 1 0.00
322 3 0.00
323 3 0.00
324 1 0.00
326 56 0.02
327 173 0.07
328 61 0.03
329 96 0.04
330 142 0.06
331 187 0.08
332 429 0.18
333 271 0.11
334 83 0.03
335 304 0.13
336 307 0.13
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (333 bp):
TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAA
TCTTTTTGGACTTGAATTATATATTTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTTTT
CGGGACAGTTTTTGCAAAATTTTGTTCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAA
CGCGTTCCTGGGCACCGACACAGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAA
ATTCATCTGACCAAATCTCAGCCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTAT
AATTCGAT
Done.